Molecular detection of respiratory coinfections in pig herds with enzootic pneumonia: a survey in Brazil.

Mycoplasma hyopneumoniae is the primary etiologic agent of swine enzootic pneumonia (EP), in which the immune response is reduced, making pigs susceptible to secondary infections. We surveyed commercial pig herds in Brazil for viral and bacterial respiratory coinfections that could complicate EP. Over a 2-y period (2015-2016), we found that 854 of 2,206 pigs (38.7%) were positive for M. hyopneumoniae in herds from various production systems in 3 Brazilian regions (Central-West, Southeast, South). We collected samples of 321 lungs positive for M. hyopneumoniae from 169 farms to also screen for Pasteurella multocida, Actinobacillus pleuropneumoniae, Glaesserella parasuis, influenza A virus (IAV), and porcine circovirus 2 (PCV2) by real-time PCR. The prevalence of pathogens found in addition to M. hyopneumoniae varied: P. multocida (141; 43.9%), G. parasuis (71; 22.1%), PCV2 (50; 15.6%), IAV (23; 7.2%), and A. pleuropneumoniae (18; 5.6%). G. parasuis was more frequent in farrowing or nursery herds (48.7%) than in breeding and fattening herds (10% and 18.6%, respectively; p < 0.01); A. pleuropneumoniae was found only in herds on farrow-to-finish and fattening farms.

Comparison of macroscopy, histopathology and PCR for diagnosing Eimeria spp. in broiler chickens / Comparação da macroscopia, histopatologia e PCR para o diagnóstico de Eimeria spp. em frangos de corte

Coccidiosis is a disease of great importance in industrial poultry. The correct diagnosis directs the poultry industry to its best treatment and control. Thus, a survey of Eimeria spp. was carried out in intestines of 64 broiler flocks, with an average age of 29 days. Eight broilers from each flock were randomly removed from the slaughter line, in a total of 512 samples. Macroscopic and histopathological lesions in the intestine were classified into Scores 0 to 4. Polymerase chain reaction (PCR) was used to research the oocysts from the seven species of Eimeria spp. in the intestinal content. The macroscopic evaluations showed that 59.4% (38/64) of the flocks were positive for E. acervulina, 32.8% (21/64) for E. maxima, 29.7% (19/64) for E. tenella, and 34.4% (22/64) for E. brunetti. The histopathological evaluation showed that 87.5% (56/64) of the flocks had at least one broiler with parasitic structures compatible with Eimeria spp. in the duodenum, 70.3% (45/64) in the jejunum, 18.8% (12/64) in the ileum, 46.9% (30/64) in the cecum, and 4.7% (3/64) in the colon. In PCR, 21.9% (14/64) of the flocks were positive for E. acervulina, 12.5% (8/64) for E. maxima, 3.1% (2/64) for E. mitis, and 32.8% (21/64) for E. tenella. The Kappa Cohen test between macroscopy, histopathology, and PCR demonstrated concordance ranging from weak to moderate with the exception of histopathology and PCR of the cecum, which was strong. In the comparison between macroscopy and histopathology, there were significative differences between Scores 0 and 1 (apart from the cecum). For Score 3, there were significative differences in duodenum, jejunum and cecum (p<0.05). In conclusion, the macroscopic diagnosis and PCR can generate false-negative results, and the histopathological exam proved to be effective, making it essential to associate different techniques for the correct diagnosis of Eimeria spp. in broiler chickens.

A coccidiose é uma doença de grande importância na avicultura industrial. O diagnóstico correto direciona a indústria avícola ao seu melhor tratamento e controle. Desta forma, realizou-se a pesquisa de Eimeria spp. em intestinos de 64 lotes de frangos de corte, com idade média de 29 dias. Em cada lote foram retirados aleatoriamente oito frangos da linha de abate, totalizando 512. Os intestinos foram classificados na macroscopia e na histopatologia em Grau de 0 a 4. No conteúdo intestinal pesquisou-se por reação em cadeia da polimerase (PCR) oocistos das sete espécies de Eimeria. As avaliações macroscópicas demonstraram que 59,4% (38/64) dos lotes foram positivos para E. acervulina, 32,8% (21/64) para E. maxima, 29,7% (19/64) para E. tenella e 34,4% (22/64) para E. brunetti. Na avaliação histopatológica, 87,5% (56/64) dos lotes apresentaram pelo menos um frango com estruturas parasitárias compatíveis com Eimeria spp. no duodeno, 70,3% (45/64) no jejuno, 18,8% (12/64) no íleo, 46,9% (30/64) no ceco e 4,7% (3/64) no cólon. Na PCR 21,9% (14/64) dos lotes foram positivos para E. acervulina, 12,5% (8/64) para E. maxima, 3,1% (2/64) para E. mitis e 32,8% (21/64) para E. tenella. O teste de concordância de Kappa Cohen entre macroscopia, histopatologia e PCR demonstrou concordância variando de fraca a moderada com exceção da histopatologia e PCR do ceco que foi forte. Na comparação dos graus de macroscopia e histopatologia, foram encontradas diferenças significativas entre o Grau 0 e 1 (exceto no ceco) e no Grau 3 houve diferença para duodeno, jejuno e cecos (p<0,05). Conclui-se que o diagnóstico macroscópico e a PCR podem gerar resultados falsos negativos e que o exame histopatológico se demostrou eficaz, tornando fundamental a associação de diferentes técnicas para o correto diagnóstico de Eimeria spp. em frangos de corte.

Comparison of macroscopy, histopathology and PCR for diagnosing Eimeria spp. in broiler chickens

ABSTRACT: Coccidiosis is a disease of great importance in industrial poultry. The correct diagnosis directs the poultry industry to its best treatment and control. Thus, a survey of Eimeria spp. was carried out in intestines of 64 broiler flocks, with an average age of 29 days. Eight broilers from each flock were randomly removed from the slaughter line, in a total of 512 samples. Macroscopic and histopathological lesions in the intestine were classified into Scores 0 to 4. Polymerase chain reaction (PCR) was used to research the oocysts from the seven species of Eimeria spp. in the intestinal content. The macroscopic evaluations showed that 59.4% (38/64) of the flocks were positive for E. acervulina, 32.8% (21/64) for E. maxima, 29.7% (19/64) for E. tenella, and 34.4% (22/64) for E. brunetti. The histopathological evaluation showed that 87.5% (56/64) of the flocks had at least one broiler with parasitic structures compatible with Eimeria spp. in the duodenum, 70.3% (45/64) in the jejunum, 18.8% (12/64) in the ileum, 46.9% (30/64) in the cecum, and 4.7% (3/64) in the colon. In PCR, 21.9% (14/64) of the flocks were positive for E. acervulina, 12.5% (8/64) for E. maxima, 3.1% (2/64) for E. mitis, and 32.8% (21/64) for E. tenella. The Kappa Cohen test between macroscopy, histopathology, and PCR demonstrated concordance ranging from weak to moderate with the exception of histopathology and PCR of the cecum, which was strong. In the comparison between macroscopy and histopathology, there were significative differences between Scores 0 and 1 (apart from the cecum). For Score 3, there were significative differences in duodenum, jejunum and cecum (p 0.05). In conclusion, the macroscopic diagnosis and PCR can generate false-negative results, and the histopathological exam proved to be effective, making it essential to associate different techniques for the correct diagnosis of Eimeria spp. in broiler chickens.

RESUMO: A coccidiose é uma doença de grande importância na avicultura industrial. O diagnóstico correto direciona a indústria avícola ao seu melhor tratamento e controle. Desta forma, realizou-se a pesquisa de Eimeria spp. em intestinos de 64 lotes de frangos de corte, com idade média de 29 dias. Em cada lote foram retirados aleatoriamente oito frangos da linha de abate, totalizando 512. Os intestinos foram classificados na macroscopia e na histopatologia em Grau de 0 a 4. No conteúdo intestinal pesquisou-se por reação em cadeia da polimerase (PCR) oocistos das sete espécies de Eimeria. As avaliações macroscópicas demonstraram que 59,4% (38/64) dos lotes foram positivos para E. acervulina, 32,8% (21/64) para E. maxima, 29,7% (19/64) para E. tenella e 34,4% (22/64) para E. brunetti. Na avaliação histopatológica, 87,5% (56/64) dos lotes apresentaram pelo menos um frango com estruturas parasitárias compatíveis com Eimeria spp. no duodeno, 70,3% (45/64) no jejuno, 18,8% (12/64) no íleo, 46,9% (30/64) no ceco e 4,7% (3/64) no cólon. Na PCR 21,9% (14/64) dos lotes foram positivos para E. acervulina, 12,5% (8/64) para E. maxima, 3,1% (2/64) para E. mitis e 32,8% (21/64) para E. tenella. O teste de concordância de Kappa Cohen entre macroscopia, histopatologia e PCR demonstrou concordância variando de fraca a moderada com exceção da histopatologia e PCR do ceco que foi forte. Na comparação dos graus de macroscopia e histopatologia, foram encontradas diferenças significativas entre o Grau 0 e 1 (exceto no ceco) e no Grau 3 houve diferença para duodeno, jejuno e cecos (p 0,05). Conclui-se que o diagnóstico macroscópico e a PCR podem gerar resultados falsos negativos e que o exame histopatológico se demostrou eficaz, tornando fundamental a associação de diferentes técnicas para o correto diagnóstico de Eimeria spp. em frangos de corte.

Comparison of macroscopy, histopathology and PCR for diagnosing Eimeria spp. in broiler chickens / Comparação da macroscopia, histopatologia e PCR para o diagnóstico de Eimeria spp. em frangos de corte

Coccidiosis is a disease of great importance in industrial poultry. The correct diagnosis directs the poultry industry to its best treatment and control. Thus, a survey of Eimeria spp. was carried out in intestines of 64 broiler flocks, with an average age of 29 days. Eight broilers from each flock were randomly removed from the slaughter line, in a total of 512 samples. Macroscopic and histopathological lesions in the intestine were classified into Scores 0 to 4. Polymerase chain reaction (PCR) was used to research the oocysts from the seven species of Eimeria spp. in the intestinal content. The macroscopic evaluations showed that 59.4% (38/64) of the flocks were positive for E. acervulina, 32.8% (21/64) for E. maxima, 29.7% (19/64) for E. tenella, and 34.4% (22/64) for E. brunetti. The histopathological evaluation showed that 87.5% (56/64) of the flocks had at least one broiler with parasitic structures compatible with Eimeria spp. in the duodenum, 70.3% (45/64) in the jejunum, 18.8% (12/64) in the ileum, 46.9% (30/64) in the cecum, and 4.7% (3/64) in the colon. In PCR, 21.9% (14/64) of the flocks were positive for E. acervulina, 12.5% (8/64) for E. maxima, 3.1% (2/64) for E. mitis, and 32.8% (21/64) for E. tenella. The Kappa Cohen test between macroscopy, histopathology, and PCR demonstrated concordance ranging from weak to moderate with the exception of histopathology and PCR of the cecum, which was strong. In the comparison between macroscopy and histopathology, there were significative differences between Scores 0 and 1 (apart from the cecum). For Score 3, there were significative differences in duodenum, jejunum and cecum (p<0.05). In conclusion, the macroscopic diagnosis and PCR can generate false-negative results, and the histopathological exam proved to be effective, making it essential to associate different techniques for the correct diagnosis of Eimeria spp. in broiler chickens.(AU)

A coccidiose é uma doença de grande importância na avicultura industrial. O diagnóstico correto direciona a indústria avícola ao seu melhor tratamento e controle. Desta forma, realizou-se a pesquisa de Eimeria spp. em intestinos de 64 lotes de frangos de corte, com idade média de 29 dias. Em cada lote foram retirados aleatoriamente oito frangos da linha de abate, totalizando 512. Os intestinos foram classificados na macroscopia e na histopatologia em Grau de 0 a 4. No conteúdo intestinal pesquisou-se por reação em cadeia da polimerase (PCR) oocistos das sete espécies de Eimeria. As avaliações macroscópicas demonstraram que 59,4% (38/64) dos lotes foram positivos para E. acervulina, 32,8% (21/64) para E. maxima, 29,7% (19/64) para E. tenella e 34,4% (22/64) para E. brunetti. Na avaliação histopatológica, 87,5% (56/64) dos lotes apresentaram pelo menos um frango com estruturas parasitárias compatíveis com Eimeria spp. no duodeno, 70,3% (45/64) no jejuno, 18,8% (12/64) no íleo, 46,9% (30/64) no ceco e 4,7% (3/64) no cólon. Na PCR 21,9% (14/64) dos lotes foram positivos para E. acervulina, 12,5% (8/64) para E. maxima, 3,1% (2/64) para E. mitis e 32,8% (21/64) para E. tenella. O teste de concordância de Kappa Cohen entre macroscopia, histopatologia e PCR demonstrou concordância variando de fraca a moderada com exceção da histopatologia e PCR do ceco que foi forte. Na comparação dos graus de macroscopia e histopatologia, foram encontradas diferenças significativas entre o Grau 0 e 1 (exceto no ceco) e no Grau 3 houve diferença para duodeno, jejuno e cecos (p<0,05). Conclui-se que o diagnóstico macroscópico e a PCR podem gerar resultados falsos negativos e que o exame histopatológico se demostrou eficaz, tornando fundamental a associação de diferentes técnicas para o correto diagnóstico de Eimeria spp. em frangos de corte.(AU)

Prevalence of Eimeria sp. in Broiler Poultry Houses with Positive and Negative Pressure Ventilation Systems in Southern Brazil.

Coccidiosis is an enteric disease caused by protozoa of the Eimeria genus and is of great economic relevance in industrial aviculture. The objective of this work was to determine the prevalence of Eimeria sp. in broiler poultry houses with positive (System 1) and negative (System 2) pressure ventilation and assess the associated factors. A transversal study was conducted using 8 random broiler chickens from 64 houses (n = 512) and macroscopic and histologic evaluation of the intestines, as well as PCR for Eimeria sp. The prevalence of Eimeria sp. was 90.6% (95% confidence interval [CI]: 97.8-83.5), with 93.8% (95% CI: 100-85.4) in System 1 and 87.5% (95% CI: 99.0-76.0) in System 2. The most prevalent species was Eimeria acervulina, and the most common combination was Eimeria acervulina, Eimeria maxima, and Eimeria tenella. System 2 and the negative Eimeria subgroup showed the best results for feed conversion and daily weight gain. By evaluating litter treatment, we found that quicklime reduced the risk of presence of Eimeria maxima and Eimeria tenella. In conclusion, Eimeria sp. had a high prevalence in both systems, with a predominance of mixed infections. System 2 and negative flocks showed the best zootechnical results.

Prevalencia de Eimeria sp. en casetas de pollo de engorde con presión positiva y presión negativa. La coccidiosis es una enfermedad entérica causada por protozoos del género Eimeria. Es una enfermedad de gran relevancia económica en la avicultura industrial. El objetivo de este trabajo fue determinar la prevalencia de Eimeria sp. en gallineros de engorde con ventilación de presión positiva (sistema 1) y negativa (sistema 2) y evaluar los factores asociados. Se realizó un estudio transversal con ocho pollos de engorde de 64 galpones (n = 512) con los cuales se realizó una evaluación macroscópica e histológica de los intestinos, así como PCR para Eimeria sp. La prevalencia de Eimeria sp. fue 90,6% (95% CI: 97,8-83,5), con 93,8% (95% CI: 100-85,4) en el sistema 1 y 87,5% (95% CI: 99,0-76,0) en el sistema 2. La especie más prevalente fue Eimeria acervulina, y la combinación más común fue Eimeria acervulina, Eimeria maxima y Eimeria tenella. El sistema 2 y el subgrupo Eimeria negativo mostraron los mejores resultados para la conversión alimenticia y el aumento de peso diario. Al evaluar el tratamiento de la cama, la cal viva redujo el riesgo de presencia de Eimeria maxima y Eimeria tenella. En conclusión, Eimeria sp. tuvo una alta prevalencia en ambos sistemas, con predominio de infecciones mixtas. El sistema 2 y los lotes negativos mostraron los mejores resultados zootécnicos.

Clonality of Mycoplasma hyopneumoniae in swine farms from Brazil.

Mycoplasma hyopneumoniae causes enzootic pneumonia (EP) in swine, a disease related to high economic losses in production systems. Epidemiological spread of M. hyopneumoniae clones was studied by multi-locus sequence typing (MLST) in several swine production regions but so far not in South America. Using MLST, we have therefore investigated M. hyopneumoniae clones circulating in farms from three main swine production regions in Brazil. Porcine lungs samples were collected between 2015 and 2016 in farms with EP outbreaks. Three geographically distant regions were selected, and 67 M. hyopneumoniae positive samples, each one from a different farm, were included in the study. The occurrence of five sequence types (ST) was demonstrated and the majority of the samples were identified as ST-69 (n = 60; 89.5%), followed by ST-70 (n = 3; 4.5%), ST-123 (n = 2; 3%), ST-124 (n = 1; 1.5%) and ST-127 (n = 1; 1.5%). There was no association of any specific ST with region or production system. The five STs were all new ones, probably representing unique Brazilian clones. ST-69 and ST-70 on one side and ST-123 and ST-124 on the other side are phylogenetically close, while ST-127 is singleton. In conclusion, our results showed a low variability and high clonality of M. hyopneumoniae genotypes from Brazilian farms affected by EP.

A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus.

The avian infectious bronchitis virus is classified into serotypes or genotypes (or both) in different poultry-producing countries of the world. In Brazil, Massachusetts type (Mass), used as a live vaccine, and local field Brazilian variants (genotypes; BR) predominate in the commercial poultry flocks. This study describes the development and validation of two real-time reverse-transcription polymerase chain reactions (RT-qPCR) for the specific detection of Mass and BR genotypes in allantoic fluids and clinical samples. Genotype-specific primers, combined with a generic probe targeted to the S1 gene, originated Mass RT-qPCR and BR RT-qPCR-specific assays. Analytical sensitivity and linearity of these assays were determined in comparison with an IBV generic real-time RT-PCR based on the 5' untranslated region (5'UTR RT-qPCR). Mass RT-qPCR detected five Mass field isolates, three vaccine samples, and one coinfected sample (BR and Mass) while BR RT-qPCR detected 16 BR field isolates. Both assays were linear (R(2) > 0.98), reproducible, and as sensitive as the classical 5'UTR RT-qPCR used to detect IBV. In the analysis of 141 IBV clinical samples, 8 were positive for Mass RT-qPCR, 76 for BR RT-qPCR, and 2 for both assays. In the remaining 55 samples, 25 were positive only for 5'UTR RT-qPCR and 30 were negative for the three assays. In conclusion, both assays were able to detect Mass and BR genotypes, allowing rapid and easy IBV molecular typing from allantoic fluids and clinical samples.

Infectious bronchitis virus in different avian physiological systems-a field study in Brazilian poultry flocks.

Avian infectious bronchitis is a highly contagious viral disease with economic effects on poultry agribusiness. The disease presents multi-systemic clinical signs (respiratory, renal, enteric, and reproductive) and is caused by one coronavirus (infectious bronchitis virus, IBV). Infectious bronchitis virus is classified into different serotypes and genotypes (vaccine strains and field variants). This study aimed to evaluate the occurrence of IBV in commercial poultry flocks from 3 important producing regions in Brazil and to determine the tropism of the main circulating genotypes to 3 different avian physiological systems (respiratory, digestive, urinary/reproductive). Clinical samples with suggestive signs of IBV infection were collected from 432 different poultry commercial flocks (198 from broilers and 234 from breeders). The total number of biological samples consisted of organ pools from the 3 above physiological systems obtained of farms from 3 important producing regions: midwest, northeast, and south. Infectious bronchitis virus was detected by reverse-transcription, real-time PCR of the 5' untranslated region. The results showed 179 IBV-positive flocks (41.4% of the flocks), with 107 (24.8%) from broilers and 72 (16.8%) from breeders. There were similar frequencies of IBV-positive flocks in farms from different regions of the country, most often in broilers (average 54%) compared with breeders (average 30.8%). reverse-transcription was more frequently detected in the digestive system of breeders (40%), and in the digestive (43.5%) and respiratory (37.7%) systems of broilers. Infectious bronchitis virus genotyping was performed by a reverse-transcription nested PCR and sequencing of the S1 gene from a selection of 79 IBV-positive flocks (45 from broilers and 34 from breeders). The majority of the flocks were infected with Brazilian variant genotype than with Massachusetts vaccine genotype. These results demonstrate the predominance of the Brazilian variant (mainly in the enteric tract) in commercial poultry flocks from 3 important producing regions in Brazil.

Emergence of a new genotype of avian infectious bronchitis virus in Brazil.

Infectious bronchitis virus (IBV) is the agent of a highly contagious disease that affects domestic fowl (Gallus gallus). Recent reports showed a high prevalence of one main IBV genotype (Brazil or BR-I) with low genetic diversity in commercial poultry flocks from Brazil. This research analyzed IBV positive poultry flocks from different rearing regions to verify the S1 gene variability and geographic distribution of variant IBV strains in recent years (2010 and 2011). Samples of IBV-positive flocks were obtained from 60 different farms. Forty-nine partial S1 gene sequences were determined and aligned for phylogenetic and amino acid similarity analyses. Eleven samples (22.4%) were similar to Massachusetts vaccine strains (Mass genotype) and 34 samples (69.4%) to the previously characterized Brazilian BR-I genotype. Interestingly, the remaining four samples (8.2%) clustered into a new IBV variant genotype (Brazil-II or BR-II), divergent from the BR-I. A unique nucleotide sequence insertion coding for five amino acid residues was observed in all the Brazilian variant viruses (BR-I and BR-II genotypes). These results show a higher genetic diversity in Brazilian IBV variants than previously described.